Detection of HIV-1-specific CTL responses in Clade B infection with Clade C Peptides and not Clade B consensus peptides

The variability of HIV-1 sequences within and between persons in vivo complicates immunologic screening with a fixed sequence, and using peptides based on consensus sequences therefore has become a common practice for pathogenesis and vaccine studies. Here, we screen a cohort of HIV-1-infected persons in the United States for CD8+ T lymphocyte (CTL) responses using Gag peptides based on the Clade C primary isolate DU422 and the consensus sequence for Clade B. Surprisingly, the DU422 and Clade B consensus peptides are similar in sensitivity, but many responses are detected only by one set or the other. About equal numbers of discordantly detected responses are specific to consensus Clade B peptides as DU422 peptides. A minority of discordant detection is due to the varying frames of the peptide sets and therefore a technical artifact; the majority is due to sequence differences. This lack of superiority of the Clade B consensus peptides to detect CD8+ T lymphocyte responses is an unexpected finding that suggests that detection of HIV-1-specific cellular immunity with these peptides may be significantly insensitive and raises questions as to whether screening with a single sequence adequately reflects responses to the viral swarm in vivo.